[gmx-users] Urey Bradley Parameters in GROMACS

[Justin A. Lemkul]

PRADEEP VENKATARAMAN wrote:
> Hello everyone,
> 
> I have a pdb file of a solvent molecule for which I need to generate a 
> .itp file. 
> 
> The solute is modeled using AMBER and I have topology file generated 
> using amb2gmx.sh.
> 
> However, the solvent molecule has Urey Bradley parameters specified. 
> 

Then, wouldn't the CHARMM force field be more appropriate?  Angles in AMBER do 
not usually include these terms.

> Since, I am new to GROMACS I wish to learn as to how an .itp could be 
> created from scratch to incorporate the aforesaid parameters.
> 

Please see the manual, specifically Chapter 5 and Table 5.4; as long as you have 
sound justification for using those parameters within the chosen force field, 
you can easily add them to the [angles] directive of the topology.

-Justin

> Thanks,
> 
> Pradeep 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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